Source: UNIVERSITY OF KENTUCKY submitted to
GENOMIC AND METAGENOMIC ANALYSES OF A WOOD-FEEDING COCKROACH, CRYPTOCERCUS PUNCTULATUS
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
Reporting Frequency
Annual
Accession No.
0220839
Grant No.
(N/A)
Project No.
KY008053
Proposal No.
(N/A)
Multistate No.
(N/A)
Program Code
(N/A)
Project Start Date
Oct 1, 2009
Project End Date
Sep 30, 2014
Grant Year
(N/A)
Project Director
Zhou, XU.
Recipient Organization
UNIVERSITY OF KENTUCKY
500 S LIMESTONE 109 KINKEAD HALL
LEXINGTON,KY 40526-0001
Performing Department
Entomology
Non Technical Summary
As readily available fossil fuels are depleted, attention has turned to lignocelluloses to convert solar energy into thermochemical energy. Lignocellulose is a naturally occurring complex of plant-derived materials that includes the hydrophilic sugar polymers cellulose and hemicellulose, and the hydrophobic organic glue lignin. However, to release the solar energy stored in plants through photosynthesis, an array of enzymes referred to as lignocellulases are required to disassociate a matrix of cellulose, hemicelluloses, pectins, lignin, and glycosidic linkages. Similar to lower termites, wood-feeding C. punctulatus and their gut symbionts have co-evolved into a suite of specialized enzymes that synergistically break down lignocelluloses. While the pressing needs for bioenergy and biomass conversion have redirected termite research to focus more on the lignocellulose degradation, research on Cryptocercus has been primarily focused on evolutionary relationships with Isoptera (termites), and the development of sociality. There is virtually no information available on lignocellulose digestion and degradation in wood-feeding cockroaches. To fill this knowledge gap and to enrich the existing gene pool of lignocellulolytic enzymes, I propose to sequence 1) a cDNA library synthesized from the entire digestive tract without symbionts, and 2) a gDNA library extracted from hindgut microbial community of the wood-feeding cockroach using a high throughput 454 pyrosequencing platform. The potential impacts of the proposed project are that 1) a complete genome-metagenome-wide survey of lignocellulases will add novel information regarding the enzymatic conversion of lignocellulosic biomass; 2) information gained from the wood-feeding cockroach may help to identify a subset of conserved lignocellulolytic enzymes throughout C. punctulatus "C R. flavipes lineage; The distribution of lignocellulase genes among different insects has yet to be explored in great detail. However, given the fact that Cryptocercus and lower termites share many flagellate symbionts such as oxymonadid and hypermastigid in their hindguts, it is germane to survey the homogeneity of lignocellulases across Dictyoptera with the basal C. punctulatus as a reference using a comparative genomic approach. Generally, evolutionarily conserved lignocellulases bear more biological meaning in the processes of lignocellulosic biomass conversion and may shed light on the core enzymes of the lignocellulose digestion machinery; 3) Cryptocercus maintains more diverse gut flagellate species than any existing termite species, and provides an invaluable resource for novel lignocellulases; and 4) it will help us to elucidate the operating mechanism underlying the host-symbiont lignocellulose digestion systems. The role that endogenous and symbiotic lignocellulases play in lignocellulose digestion has remained a point of conjecture. The proposed sequencing will shed light on the genome organization and interactions (synergistically or independently) of the existing dual lignocellulase system in both C. punctulatus and R. flavipes.
Animal Health Component
(N/A)
Research Effort Categories
Basic
(N/A)
Applied
(N/A)
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2113110102010%
2113110104020%
2113110105010%
2113110106010%
2113110113010%
2113110308010%
3043110102010%
3043110104010%
3043110106010%
Goals / Objectives
Goals The overall goals of the proposed research are to 1) inventory lignocellulases involved in digestion and degradation of woody materials in a wood-feeding cockroach, Cryptocercus punctulatus, 2) identify and characterize core lignocellulases critical for biomass enzymatic pretreatments, and 3) harness the power of advanced biotechnologies, such as protein engineering and plant-based protein production system, to mass produce lignocellulases with potential biorefinery applications. Objectives To achieve our overall goals, we are pursuing the following specific objectives using a readily available pyrosequencing technology at the University of Kentucky to: (1) conduct large-scale transcriptomic sequencing of symbiont-free C. punctulatus gut tissue, (2) carry out high-throughput metagenomic sequencing of C. punctulatus pro-and eukaryotic symbionts, (3) identify a subset of lignocellulases highly conserved among the C. punctulatus + R. flavipes clade, and initiate investigations to characterize their physical and lignocellulolytic properties, and (4) collaborate with Dr. Yuan Ling to enhance biorefinery potential of selected lignocellulolytic enzymes by directed evolution, and to demonstrate the feasibility of producing industrial scale of selected novel lignocellulases in a high-level protein production system in plants using proprietary gene expression techniques. Expected outputs Sequence utilization. The primary way in which the sequence information will be utilized is to: 1) gain a global view of lignocellulose digestion in the wood-feeding cockroach; 2) identify a suite of key genes involved in lignocellulose digestion; and 3) perform downstream applications with selected lignocellulase genes for either biomass conversion (e.g. enzymatic pretreatments) or industrial applications (detergents). There are also numerous secondary scientific outcomes that will be benefited from this endeavor, such as the evolution of lignocellulolytic enzymes in insects and development of eusociality in social animals. Community impacts. The genomics communities that will benefit from this sequencing efforts will be the International Termite Genome Consortium, Diabrotica Genetics Consortium, Honey Bee Genome Consortium, and other omics researchers who are interested in sociogenomics, lignocellulose decomposition, biomass conversion and biorefinery. The true benefit of this genomic and metagenomic sequencing effort is that it will lead C. punctulatus research into the genomic era. As a result, many more scientists are expected to be drawn into the wood-feeding cockroach research. Integration of research and education. Several aspects of the PI ongoing research program in wood-feeding insect genomics, biochemistry and physiology have direct links to undergraduate, graduate, and post-doctoral education. Dr. Zhou is seeking to continuously employ undergraduate students as summer interns or lab technicians, as well as have them work for up to 6 credits in his laboratory under a Independent study or Internship format as part of the courses offered by Agricultural Biotechnology program at the University of Kentucky (ABT 395 and ABT 399).
Project Methods
Research approach Wood-feeding cockroach lignocellulose digestion is a process contributed by endogenous cockroach-derived factors, as well as prokaryotic and eukaryotic gut endosymbionts. However, the architecture and dynamic of the endogenous and symbiotic system have been an uncharted territory for decades. Here, with the advent of novel biological tools, a genomics and metagenomics-mediated approach will be employed to better understand the framework of lignocellulose digestion machinery and digestive contributions of host and symbiont in the wood-feeding cockroach, C. punctulatus. In addition, I will investigate the industrial potential of selected core lignocellulolytic enzymes in collaboration with protein engineers from the University of Kentucky and private industry. Our approach starts with ultra-high throughput pyrosequencing from a cDNA pool synthesized from cockroach gut tissues free of symbionts and a community genomic DNA pool extracted from cockroach hindgut luminal contents, and follows by the identification and characterization of most-conserved lignocellulases between phylogentically closely related C. punctulatus and R. flavipes. Finally, a collaborative research team will test the industrial potential of selected lignocellulolytic enzymes using state-of-art protein engineering and production technologies. Sequence analysis Pyrosequencing will be carried out by the University of Kentucky Advanced Genetic Technologies Center (UKY-AGTC). A bioinformatican, Dr. Aurelian Tartar, a collaborator at the Nova Southeastern University will provide training and assistance with assembly, annotation, and interpretation of genomic and metagenomic data. The resulting genomic and metagenomic sequences from wood-feeding cockroach will be formatted and submitted to the Genbank to make it assessable to the research community at large. Potential pitfalls and contingencies Although application of 454 pyrosequencing has not been widely adopted for genomic and metagenomic sequencing, I believe this platform provides the coverage and efficiency for more complete characterization of the lignocellulose digestion in the wood-feeding C. punctulatus. The biggest limitation likely to be faced with this technique will be in the assembly and annotation of the initial raw sequence data due to the complexity and diversity of C. punctulatus hindgut symbionts. However, based on Dr. Zhou previous genomic and metagenomic sequencing experiences with termites (Zhou et al., 2007a; Tartar et al., 2009), we now have several closely related reference metagenomes and EST libraries for comparisons. Milestones and project evaluation The proposed project will be evaluated by the five milestones corresponding to the four specific objectives: 1) transcriptomic sequencing of symbiont-free C. punctulatus gut tissue, 2) metagenomic sequencing of luminal contents of C. punctulatus hindgut, 3) sequence analyses, 4) comparative genomic analysis to identify a subset of lignocellulases highly conserved among the C. punctulatus + R. flavipes clade, and finally 5) evaluate biorefinery potential of selected lignocellulolytic enzymes.

Progress 10/01/09 to 09/30/14

Outputs
Target Audience: Primary audiences: Scientists from academia and industry Secondary audiences: Stakeholders in the private, public, and non-profit sectors working on biofuels, biorefinery, and biomass conversion. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? This proposal represents a collaborative effort among scientists from the Department of Entomology, University of Kentucky (Zhou) and the Department of Plant and Soil Sciences, University of Kentucky (Yuan). Dr. Ling Yuan, a protein engineer, has been collaborating with us on the downstream functional characterization of endogenous lignocellulases from C.punctulatus digestome. Dr. Xiangrui Li was an exchange student (Zhou Lab) from the China Agricultural University, and carried out the woodroach sequencing projects between 2009-2011. Dr. Sanjay Singh is a postdoctoral researcher (Yuan Lab), and has been working on the characterization studies of candidate woodroach cellulase genes since 2012. How have the results been disseminated to communities of interest? As fossil fuels are being depleted, attention has turned to abundant carbohydrate energy resources, in particular, lignocellulose, a naturally occurring complex of plant-derived materials that includes hydrophilic sugar polymers, cellulose and hemicellulose, and a hydrophobic organic "glue"- lignin. However, to release the solar energy stored within (approximately 10 times of the current world energy consumption), an array of enzymes or lignocellulases are required to disassociate a matrix of cellulose, hemicelluloses, pectins, lignin, and glycosidic linkages. The new wave of using renewable lignocellulosic biomass including byproducts from agriculture and forestry for the production of biofuels is a vital alternative to fossil-based energy resources. However, a number of obstacles, such as the thermo-chemical conversion of biomass, must be overcome prior to achieving a sustainable production of biofuels. The potential for second-generation biofuels that can overcome critical bottlenecks associated with their use has only started to be realized in the past decade. And, this situation would be greatly improved if we understood more about wood-feeding insects, the best examples of highly efficient enzymatic lignocellulose digestive systems extant in nature. A comprehensive transcriptomic-metatranscriptomic survey of the woodroach digestome will yield highly useful and unique information regarding enzymatic conversion of lignocellulosic biomass as well as the nitrogen fixation and nitrogen recycling processes. In addition, information gained from the wood-feeding cockroach will help to identify a subset of core enzymes within the lignocellulose digestion machinery that are representative across the species and which is the key for this process. The distribution of lignocellulase genes among different insects has yet to be explored in great detail; however, there has been a recent influx of sequence information from cellulolytic insect taxa. Given the fact that Cryptocercus and lower termites share many flagellate symbionts in their hindguts, it is germane to survey the homogeneity of lignocellulases across all known Dictyopteran species (termite and woodroach) using the most basal Cryptocercus as a reference. Evolutionally conserved lignocellulases harbor significant biological information, and have great potential to shed light on the elusive core enzymes of the lignocellulose digestion machinery. Highly active and chemical/thermal stable lignocellulolytic biocatalysts are a major bottleneck for the large-scale production of biofuels from lignocellulosic biomass. This research provides a list of core enzymes fundamentally important to the degradation of woody materials, suggesting the potential applications in the biomass conversion of agricultural and forestry byproducts, as well as other industrial needs. Another point of significance for this research is that Cryptocercus maintains more diverse gut flagellate species than any existing termite species, and provides an invaluable resource for novel lignocellulases; which will allow us to better understand the host-symbiont synergy that underlies collaborative lignocellulose digestion in the woodroach and lower termites. The role that endogenous and symbiotic lignocellulases play in lignocellulose digestion has remained a point of conjecture. Additional information from an ancestral group of "prototermites", woodroach, will provide important evidence demonstrating a synergistic/collaborative lignocellulose digestion process between hosts and their symbiotic microfauna. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Wood-feeding Dictyopterans including termites and woodroaches are, by far, the most efficient lignocellulose-processing bioreactors on this planet, and have intrigued scientists for decades because of their unique capability of breaking down seemingly recalcitrant lignocelluloses efficiently and rapidly. Although our pressing need for bioenergy and biomass conversion has redirected termite research to focus more on lignocellulose digestion and degradation, there is virtually no information available on the wood-feeding cockroach, Cryptocercus, the ancestor of termites, which occupies different habitats and employs more diverse cellulolytic symbionts than termites. Despite the most recent metagenomic sequencing effort led by the Department of Energy (DOE) on an unknown termite species in the rain forest, the lack of understanding of the lignocellulose digestion/assimilation processes in wood-feeding Dictyopteran insects is an enormous gap in the knowledge due to the diversity, complexity, and intricacy of termites, woodroaches, and their respective pro- and eukaryotic symbionts. To leverage existing efforts on termite lignocellulase research, to harness the power of readily available comparative genomics tools and most importantly, to efficiently and economically gain a better understanding of lignocellulose degradation in hundreds and thousands of wood-feeding Dictyopteran species, the easiest and most efficient process is to understand their evolutionary root, the wood-feeding cockroach, Cryptocercus. Thus, rather than picking and choosing a few representatives from over 2,700 termite species, which may or may not be informative, dissecting the genomic information from the evolutionary ancestor for all termite species will provide an all important reference point for understanding the elusive lignocelluloses digestion machinery within the wood-feeding Dictyopterans. The overall goal of the proposed research is to dissect the entire lignocellulose degradation /assimilation pathway in the wood-feeding Cryptocercus at the transcriptome level, and, during the process, to discover and engineer biocatalysts suitable for biomass enzymatic pretreatment. Our central hypothesis is that the wood-feeding cockroach Cryptocercus and its symbionts represent a rich reservoir for novel lignocellulases and the resulting core enzymes that are conserved across the termite-woodroach linage are excellent candidates for the development of multifunctional biocatalysts which potentially can be applied as biomass pretreatment. To achieve our overall goals, Two independent sequencing efforts have been carried out for the during of the project: 1) tissue-specific transcriptome sequencing of the entire digestive tract, including salivary gland, foregut, midgut, and hindgut, respectively; and 2) metatranscriptome sequencing of C. punctulatus hindgut, including pro- and eukaryotic symbionts. In addition, comparative genomics analysis identified a list of lignocellulases highly conserved among the wood-feeding Dictyopterans.Among them, we enzymatically and functionally characterized a group of endogenous genes from woodroach salivary gland, including two endoglucanases,CpuEG1 and CpuEG2, and two laccases, CpuLac1and CpuLac2. The initial characterization study shows that both enzymes can act synergistically in the degradation of natural woody materials, and is likely the core enzymes within the lignocellulose digestion machinery among wood-feeding Dictyopterans. Moreover, woodroach laccases can efficiently biodegrade the reactive dye, Remazol Brilliant Blue R (RBBR), which has potential for diverse industrial applications, e.g., textile industry.

Publications

  • Type: Journal Articles Status: Published Year Published: 2011 Citation: Liu, N., X. Yan, ML Zhang, L. Xie, Q. Wang, YP Huang, X. Zhou, SY Wang, ZH Zhou. 2011. Microbiome of fungus-growing termites: a new reservoir for mining lignocellulase genes. Appl. Environ. Micro. 77: 48-56.
  • Type: Book Chapters Status: Published Year Published: 2013 Citation: Li, XR and X. Zhou. 2013. Lignocellulolytic wood-feeding Cockroach - a forgotten treasure. In: JZ Sun, SY Ding, and J Doran-Peterson (eds), Biological Conversion of Biomass for fuel and Chemicals---Exploration from natural utilization systems. Royal Society of Chemistry  Energy and Environment Series.223-236. DOI:10.1039/9781849734738-00223
  • Type: Journal Articles Status: Under Review Year Published: 2015 Citation: Li, Z, XR Li, QW Zhang, L Yuan, X Zhou. 2015. Reference gene selection for transcription profiling in the woodroach Cryptocercus punctulatus, an evolutionary link between Isoptera and Blattodea. PLoS ONE. In revision.
  • Type: Journal Articles Status: Submitted Year Published: 2015 Citation: Singh S, XR Li, X Zhou, and L Yuan. 2015. Functional characterization of host specific lignocellulolytic enzymes from woodroach, Cryptocercus punctulatus, for potential use in lignocellulosic biomass degradation and industrial application.
  • Type: Book Chapters Status: Published Year Published: 2013 Citation: Sun, J. and X. Zhou. 2013. Lignocellulolytic systems of insects and their potential for viable biofuels. In: JZ Sun, SY Ding, and J Doran-Peterson (eds), Biological Conversion of Biomass for fuel and Chemicals---Exploration from natural utilization systems. Royal Society of Chemistry  Energy and Environment Series.195-222. DOI:10.1039/9781849734738-00195


Progress 01/01/13 to 09/30/13

Outputs
Target Audience: Nothing Reported Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? This proposal represents a collaborative effort among scientists from the Department of Entomology, University of Kentucky (Zhou) and the Department of Plant and Soil Sciences, University of Kentucky (Yuan). Dr. Ling Yuan, a protein engineer, has been collaborating with us on the downstream functional characterization of endogenous lignocellulases from C. punctulatus digestome. How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals? We are on track to complete all the stated objectives which will provide answers to questions directly pertaining to the identification of a group of core enzymes fundamentally important to the degradation of woody materials.

Impacts
What was accomplished under these goals? Highly active and chemical/thermal stable lignocellulolytic biocatalysts are a major bottleneck for the large-scale production of biofuels from lignocellulosic biomass. The Wood-feeding cockroach and its hindgut microbiota provide an irreplaceable resource for the identification of core lignocellulolytic enzymes conserved across the woodroach - termite lineage. The distribution of lignocellulase genes among different insects has yet to be explored in great detail; however, there is a recent influx of sequence information from cellulolytic insect taxa. Given the fact that Cryptocercus and lower termites share many flagellate symbionts such as oxymonadid and hypermastigid in their hindguts, it is germane to survey the homogeneity of lignocellulases across Dictyoptera with the basal C. punctulatus as a reference. Evolutionarily conserved lignocellulases will shed light on the discovery of lignocellulose digestion machinery. The research will directly assist in the searching for the novel biocatalysts for the biomass conversion of agricultural and forestry byproducts, as well as other industrial applications. Because of its ancestral status, and the diverse cellulolytic microbial fauna shared with extant termites, Cryptocercus punctulatus represents the best available taxonomic reference to identify evolutionary conserved lignocellulases within wood-feeding dictyopterans, the most efficient bioreactors in the world. Based on the annotated C. punctulatus digestome including four transcriptomes representing salivary gland, foregut, midgut, and hindgut (without symbionts), respectively, and a hindgut microbiota metatranscriptome, we are able to identify a group of enzymes fundamentally important to the degradation of woody materials using comparative genomics tools. Among these highly conserved lignocellulases, we functionally characterized a group of endogenous genes from C. punctulatus, including two endoglucanases, CpuEG1 and CpuEG2, and two laccases, CpuLac1and CpuLac2. The initial characterization study shows that both enzymes can act synergistically in the degradation of natural woody materials. Woodroach laccases can efficiently biodegrade the reactive dye, which has potential for diverse industrial applications.

Publications

  • Type: Book Chapters Status: Published Year Published: 2014 Citation: Sun, J. and X. Zhou. 2014. Lignocellulolytic systems of insects and their potential for viable biofuels. In: JZ Sun, SY Ding, and J Doran-Peterson (eds), Biological Conversion of Biomass for fuel and Chemicals---Exploration from natural utilization systems. Royal Society of Chemistry  Energy and Environment Series. 195-222. DOI:10.1039/9781849734738-00195
  • Type: Book Chapters Status: Published Year Published: 2014 Citation: Li, XR and X. Zhou. 2013. Lignocellulolytic wood-feeding Cockroach - a forgotten treasure. In: JZ Sun, SY Ding, and J Doran-Peterson (eds), Biological Conversion of Biomass for fuel and Chemicals---Exploration from natural utilization systems. Royal Society of Chemistry  Energy and Environment Series. 223-236. DOI:10.1039/9781849734738-00223


Progress 01/01/12 to 12/31/12

Outputs
OUTPUTS: The obligate relationship of both the wood-feeding cockroach Cryptocercus and lower termites with lignocellulolytic flagellate protists in their hindguts has long been a textbook example of symbiosis. Cryptocercus is the sister group to Isoptera, and shares many similarities with lower termite taxa: 1) both feed on recalcitrant lignocelluloses (i.e., are xylophagous), 2) both exhibit an obligate relationship with hindgut symbionts, with many common flagellate genera co-occurring in both groups, 3) both are equipped with endogenous and symbiotic lignocellulases, 4) both transfer symbionts to conspecifics via proctodeal trophallaxis, and 5) both exhibit similar advanced social behaviors such as long-lasting biparental care. Although research on Cryptocercus has always been intimately related to termites because of their intertwined relationships, the current research emphases of the two sister-taxa are different. Wood-feeding insects have intrigued scientists for decades because of their unique capability of breaking down the matrix of cellulose, hemicelluloses, and lignin in plant cell walls. Lignocellulose depolymerization is a complex enzymatic process that involves an intricate collaboration between host organisms and their symbionts (pro- and eukaryotes). While the pressing needs for bioenergy and biomass conversion have redirected termite research to focus more on the lignocellulose digestion, research on Cryptocercus has been primarily focused on their phylogenetic relationship with Isoptera (termites), and the evolution of sociality. Currently, there is no genomic resource available for woodroaches, and virtually no information exists for the lignocellulose digestion and degradation in this extremely efficient wood-feeding insect species. To establish genomic baseline and to enrich the existing gene pool of lignocellulolytic enzymes, we first pyrosequenced and annotated the digestome of a wood-feeding cockroach, Cryptocercus punctulatus, including four cDNA libraries synthesized from the entire digestive tract of C. punctulatus covering salivary gland, foregut, midgut, and hindgut (without symbionts), respectively, and a metagenomic DNA library extracted from the hindgut microbial community. Most recently, in collaboration with Dr. Ling Yuan, a protein engineer at the University of Kentucky, we have screened, cloned, and functionally characterized three lignocellulases from C. punctulatus digestome. PARTICIPANTS: Dr. Ling Yuan, a protein engineer from Department of Plant and Soil Science at the University of Kentucky, has been collaborating with us on the downstream functional characterization of lignocellulases from C. punctulatus digestome. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Using more advanced bioinformatic tools, we reassembled and reannotated the C. punctulatus digestome including four transcriptomes representing salivary gland, foregut, midgut, and hindgut (without symbionts), respectively, and a hindgut microbiota metatranscriptome. In addition, we have integrated the singletons in our sequence analyses instead of using contigs or isotigs exclusively in our initial analyses in 2011. Besides three publications, manuscripts documenting in-depth bioinformatic analyses of the entire woodroach digestome are currently in preparation. More importantly, in collaboration with Dr. Ling Yuan, we have validated, cloned, and functionally characterized three lignocellulolytic genes from C. punctulatus digestome.

Publications

  • Sun, J. and X. Zhou. 2013. Lignocellulolytic systems of insects and their potential for viable biofuels. In: JZ Sun, SY Ding, and J Doran-Peterson (eds), Biological Conversion of Biomass for fuel and Chemicals-Exploration from natural utilization systems. Royal Society of Chemistry-Energy and Environment Series. In press.
  • Li, XR and X. Zhou. 2013. Lignocellulolytic wood-feeding Cockroach - a forgotten treasure. In: JZ Sun, SY Ding, and J Doran-Peterson (eds), Biological Conversion of Biomass for fuel and Chemicals-Exploration from natural utilization systems. Royal Society of Chemistry-Energy and Environment Series. In press.
  • Li, Zb, XR Li, QW Zhang, L Yuan, X Zhou. 2013. Reference gene selection for transcription profiling in the woodroach Cryptocercus punctulatus, an evolutionary link between Isoptera and Blattodea. PLoS ONE. In revision.


Progress 01/01/11 to 12/31/11

Outputs
OUTPUTS: The obligate relationship of both the wood-eating cockroach Cryptocercus and lower termites with lignocellulolytic flagellate protists in their hindguts has long been a textbook example of symbiosis. Cryptocercus is the sister group to Isoptera, and shares many similarities with lower termite taxa: 1) both feed on recalcitrant lignocelluloses (i.e., are xylophagous), 2) both exhibit an obligate relationship with hindgut symbionts, with many common flagellate genera co-occurring in both groups, 3) both are equipped with endogenous and symbiotic lignocellulases, 4) both transfer symbionts to conspecifics via proctodeal trophallaxis, and 5) both exhibit similar advanced social behaviors such as long-lasting biparental care. Although research on Cryptocercus has always been intimately related to termites because of their intertwined relationships, the current research emphases of the two sister-taxa are different. Wood-feeding insects have intrigued scientists for decades because of their unique capability of breaking down the matrix of cellulose, hemicelluloses, and lignin in plant cell walls. Lignocellulose depolymerization is a complex enzymatic process that involves an intricate collaboration between host organisms and their symbionts (pro- and eukaryotes). Although our knowledge of termite lignocellulose degradation is very limited, a recent metagenomic inventory of the microbiota from the hindgut of a higher termite sheds light on the potential role prokaryotic symbionts play in lignocellulose deploymerization, hydrogen metabolism, carbon dioxide reductive acetogenesis, and nitrogen fixation. While the pressing needs for bioenergy and biomass conversion have redirected termite research to focus more on the lignocellulose digestion, research on Cryptocercus has been primarily focused on evolutionary relationships with Isoptera (termites), and the development of sociality. There is virtually no information available on lignocellulose digestion and degradation in woodroaches. To fill this knowledge gap and to enrich the existing gene pool of lignocellulolytic enzymes, we sequenced and annotated 1) a cDNA library synthesized from the entire digestive tract including salivary gland, foregut, midgut, and hindgut (without symbionts), and 2) a genomic DNA (gDNA) library extracted from hindgut microbial community of a wood-eating cockroach, C. punctulatus, using a high-throughput 454 pyrosequencing platform. PARTICIPANTS: Dr. Xiangrui Li was an exchange student from the China Agricultural University, and has been working on the woodroach sequencing project for the past two years. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Transcriptomic analysis of C. punctulatus digestive tract: Tissue-specific transcriptomes were sequenced at the University of Arizona Genetics Core. Salivary gland, foregut, midgut, and hindgut, respectively, from 30 adult roaches were dissected and pooled for the total RNA extraction. Each woodroach tissue accounted for 1/8 of a sequencing plate. The assemblies were accomplished using Roche 454's GS De Novo Assembler Software (version 2.3). A total number of unigenes (isotigs + singletons) from 4 tissue-based libraries are 82,805, 46,705, 102,784, and 112,821, respectively. BlastX database was used to annotate resulting isotigs. The cut-off E-value was 10-6. Sequences associated with carbohydrate catabolism were classified according to the CAZy nomenclature (http://www.cazy.org/). Metatranscriptomic analysis of hindgut microbiota in C. punctulatus: Hindgut metatranscriptome were pyrosequenced by the Advanced Genetic Technologies Center (AGTC) at the University of Kentucky. Digestive tract from seven C. punctulatus adults (3 males, 4 females) was removed, and the luminal contents from hindgut were collected for sequencing. The total numbers of Reads and Bases from a half plate run are 1,010,243 and 228,975,825, respectively. The initial assembly step was to build a blast database of adapters used in the creation of library. After this, each read was blasted against this database using stringent settings to maximize the matching sequences. After blast was completed, the results were parsed and sorted in order to determine where each individual read should be trimmed. The results of this analysis were written in a format that allowed the creation of a new trimmed sff file from the original 454 run. This was done because Newbler does not take quality scores into consideration when using the FASTA files. After sequences trimmed and in sff format, Newbler was used to assemble the reads as normal. A total number of unigenes from symbiont library is 110,147. Based on the distribution profiles of carbohydrate active genes among different tissues and hindgut microbiota, endogenous lignocellulolytic enzymes are predominantly located at the salivary glands. Sequence assembly and annotation: The main goal for 2011 was to annotate C. punctulatus digestive tissue-specific transcriptomes and hindgut metatranscriptome. The initial assembly and annotation have been concluded, and we now shift our focus to 1) carry out in-depth bioinformatic analysis of the entire woodroach digestome, 2) validate the initial annotation, manually curate, and clone the lignocellulolytic genes of interest, 3) functionally characterize selected lignocellulolytic enzymes in collaboration with Dr. Ling Yuan.

Publications

  • Liu, N., X. Yan, ML Zhang, L. Xie, Q. Wang, YP Huang, X. Zhou, SY Wang, ZH Zhou. 2011. Microbiome of fungus-growing termites: a new reservoir for mining lignocellulase genes. Appl. Environ. Micro. 77: 48-56.


Progress 01/01/10 to 12/31/10

Outputs
OUTPUTS: Dictyopterans including termites and woodroaches by far are the most efficient lignocellulose-digesting bioreactors on this planet, and have intrigued scientists for decades because of their unique capability of breaking down seemingly recalcitrant lignocelluloses. In the first year of this hatch project, we initiated several sequencing projects to inventory a comprehensive set of genes encoding lignocellulases in the wood-feeding C. punctulatus. 1. Transcriptomic analysis of C. punctulatus digestive tract Tissue-specific transcriptomes were sequenced at the University of Arizona Genetics Core. Salivary gland, foregut, midgut, and hindgut, respectively, from 30 adult roaches were dissected and pooled for the total RNA extraction. Emulsion PCR (emPCR) and 454 Pyrosequencing were carried out according to Roche GS FLX Titanium protocols. Each woodroach tissue accounted for 1/8 of a sequencing plate, and the average total reads and total bases from these digestive tract tissues was 165,120 and 60,819,523, respectively. A total number of Isotigs from 4 tissue-based libraries are 1730, 4498, 3152, and 4560, respectively. 2. Metatranscriptomic analysis of hindgut microbiota in C. punctulatus Pyrosequencing of the woodroach hindgut metatranscriptome were performed by the Advanced Genetic Technologies Center (AGTC) at the University of Kentucky. Digestive tract from seven C. punctulatus adults was removed, and the luminal contents from hindgut were collected carefully. The total numbers of Reads and Bases from a half plate run are 1,010,243 and 228,975,825, respectively. A total number of Isotigs from symbiont librarys is 11,584. In comparison to the lower termite, R. flavipes, symbiotic lignocellulolytic enzymes in the woodroach hindgut microbiota (170) is significantly more abundant and diverse. 3. Metaproteomic profiling of hindgut microbiota in C. punctulatus The luminal contents collected from a total of nine C. punctulatus adults were used for metaproteomics analyses. Total protein was extracted directly from the luminal contents, and then it was subjected to the trypsin digestion, and followed by peptide identification using MALDI-TOF/TOF mass spectrometry. A total of 694 and 565 proteins were identified from C. punctulatus hindgut microbiota using peptide libraries from R. flavipes symbionts and guts, respectively. Among them, 194 and 169 sequences were unclassified. Based on the GO term molecular function, 79 peptide sequences were putatively classified as glycoside hydrolases in which majority of them belonged to GHF-7,-8, -2, -3, -5, and -18 (66 derived from the symbiont library and 13 came from the gut Library, respectively). Hindgut microbiota from C. punctulatus and R. flavipes apparently shared some lignocellulolytic enzymes (e.g. GHF-7), however the low degree of overlapping GHFs in the preliminary metaproteomics study supported the contention that C. punctulatus is a rich reservoir for novel lignocellulases. PARTICIPANTS: Xiangrui Li Department of Entomology University of Kentucky S-225 Agricultural Science Center North Lexington, KY 40546 xiangruili@uky.edu; Yuan Ling Plant Physiology Program Department of Plant and Soil Sciences, KTRDC University of Kentucky 1401 University Drive, Lexington, KY 40546 lyuan3@uky.edu; Scott M Geib Tropical Crop and Commodity Protection Research Research Entomologist 64 NOWELO STREET HILO, HI, 96720 scott.geib@ars.usda.gov TARGET AUDIENCES: This biofuel-inspired research is not only targeted at the scientific community and private sector, it is also intended for the general public as well. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
This project has considerable potential economic impacts in biomass conversion and process applications. Because of their unique biology and physiology, wood-feeding Dictyopterans provide a rich reservoir for novel lignocellulases, especially the enzymes associated with biomass pretreatments. The enzymatic pretreatment is a critical step to improve the efficiency of current biomass conversion process.

Publications

  • Sun, J. and X. Zhou. 2010. Utilization of lignocellulose-feeding Insects for viable biofuels: an emerging and promising area of entomological science. In: T. X. Liu and L. Kang (eds), Recent advances in entomological research: from molecular biology to pest management. High Education Press, Beijing, China. In press.