Computational Challenges in Characterization of Bacteria and Bacteria-Host Interactions Based on Genomic Data

Abstract Background Although extensive breeding efforts are ongoing in sugarcane (Saccharum officinarum L.), the average yield is far below the theoretical potential. Tillering is an important component of sugarcane yield, however, the molecular mechanism underlying tiller development is still elusive. The limited genomic data in sugarcane, particularly due to its complex and large genome, has hindered in-depth molecular studies. Results Herein, we generated full-length (FL) transcriptome from developing leaf and tiller bud samples based on PacBio Iso-Seq. In addition, we performed RNA-seq from tiller bud samples at three developmental stages (T0, T1 and T2) to uncover key genes and biological pathways involved in sugarcane tiller development. In total, 30,360 and 20,088 high-quality non-redundant isoforms were identified in leaf and tiller bud samples, respectively, representing 41,109 unique isoforms in sugarcane. Likewise, we identified 1063 and 1037 alternative splicing events identified in leaf and tiller bud samples, respectively. We predicted the presence of coding sequence for 40,343 isoforms, 98% of which was successfully annotated. Comparison with previous FL transcriptomes in sugarcane revealed 2963 unreported isoforms. In addition, we characterized 14,946 SSRs from 11,700 transcripts and 310 lncRNAs. By integrating RNA-seq with the FL transcriptome, 468 and 57 differentially expressed genes (DEG) were identified in T1vsT0 and T2vsT0, respectively. Strong up-regulation of several pyruvate phosphate dikinase and phosphoenolpyruvate carboxylase genes suggests enhanced carbon fixation and protein synthesis to facilitate tiller growth. Similarly, up-regulation of linoleate 9S-lipoxygenase and lipoxygenase genes in the linoleic acid metabolism pathway suggests high synthesis of key oxylipins involved in tiller growth and development. Conclusions Collectively, we have enriched the genomic data available in sugarcane and provided candidate genes for manipulating tiller formation and development, towards productivity enhancement in sugarcane.

Download Full-text

The Clash of Microbiomes: From the Food Matrix to the Host Gut

Microorganisms ◽

10.3390/microorganisms10010116 ◽

2022 ◽

Vol 10 (1) ◽

pp. 116

Author(s):

Despoina Eugenia Kiousi ◽

Nikos Chorianopoulos ◽

Chrysoula C. Tassou ◽

Alex Galanis

Keyword(s):

Raw Materials ◽

Interdisciplinary Collaboration ◽

Health Benefit ◽

Potential Health ◽

Empirical Observation ◽

New Era ◽

Host Interactions ◽

Beneficial Effects ◽

Organoleptic Characteristics

Food fermentation has led to the improvement of the safety characteristics of raw materials and the production of new foodstuffs with elevated organoleptic characteristics. The empirical observation that these products could have a potential health benefit has garnered the attention of the scientific community. Therefore, several studies have been conducted in animal and human hosts to decipher which of these products may have a beneficial outcome against specific ailments. However, despite the accumulating literature, a relatively small number of products have been authorized as ‘functional foods’ by regulatory bodies. Data inconsistency and lack of in-depth preclinical characterization of functional products could heavily contribute to this issue. Today, the increased availability of omics platforms and bioinformatic algorithms for comprehensive data analysis can aid in the systematic characterization of microbe–microbe, microbe–matrix, and microbe–host interactions, providing useful insights about the maximization of their beneficial effects. The incorporation of these platforms in food science remains a challenge; however, coordinated efforts and interdisciplinary collaboration could push the field toward the dawn of a new era.

Download Full-text

Virus-host interactions for Bluetongue virus and characterization of a new NS3 function

Access Microbiology ◽

10.1099/acmi.imav2019.po0004 ◽

2019 ◽

Vol 1 (10) ◽

Author(s):

Marie POURCELOT ◽

Cindy Kundlacz ◽

Grégory Caignard ◽

Aurore Fablet ◽

Rayane Amaral Da Silva Moraes ◽

...

Keyword(s):

Bluetongue Virus ◽

Host Interactions

Download Full-text

Co-expression networks for plant biology: why and how

Acta Biochimica et Biophysica Sinica ◽

10.1093/abbs/gmz080 ◽

2019 ◽

Vol 51 (10) ◽

pp. 981-988 ◽

Cited By ~ 6

Author(s):

Xiaolan Rao ◽

Richard A Dixon

Keyword(s):

Gene Expression ◽

Network Analysis ◽

Expression Analysis ◽

Expression Profiling ◽

Recent Literature ◽

Genomic Data ◽

Relevant Information ◽

Plant Biology ◽

Biologically Relevant

Abstract Co-expression network analysis is one of the most powerful approaches for interpretation of large transcriptomic datasets. It enables characterization of modules of co-expressed genes that may share biological functional linkages. Such networks provide an initial way to explore functional associations from gene expression profiling and can be applied to various aspects of plant biology. This review presents the applications of co-expression network analysis in plant biology and addresses optimized strategies from the recent literature for performing co-expression analysis on plant biological systems. Additionally, we describe the combined interpretation of co-expression analysis with other genomic data to enhance the generation of biologically relevant information.

Download Full-text

Characterization of Insect Immune Systems from Genomic Data

Springer Protocols Handbooks - Immunity in Insects ◽

10.1007/978-1-0716-0259-1_1 ◽

2020 ◽

pp. 3-34 ◽

Cited By ~ 1

Author(s):

Robert M. Waterhouse ◽

Brian P. Lazzaro ◽

Timothy B. Sackton

Keyword(s):

Genomic Data ◽

Immune Systems

Download Full-text

The Pathogen-Host Interactions Database (PHI-base) Provides Insights into Generic and Novel Themes of Pathogenicity

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-19-1451 ◽

2006 ◽

Vol 19 (12) ◽

pp. 1451-1462 ◽

Cited By ~ 53

Author(s):

Thomas K. Baldwin ◽

Rainer Winnenburg ◽

Martin Urban ◽

Chris Rawlings ◽

Jacob Koehler ◽

...

Keyword(s):

Comparative Genomics ◽

Virulence Genes ◽

Host Responses ◽

Plant Responses ◽

Avirulence Genes ◽

Pathogenicity Genes ◽

Host Interactions ◽

Effector Genes ◽

Computational Resources

Fungal and oomycete pathogens of plants and animals are a major global problem. In the last 15 years, many genes required for pathogenesis have been determined for over 50 different species. Other studies have characterized effector genes (previously termed avirulence genes) required to activate host responses. By studying these types of pathogen genes, novel targets for control can be revealed. In this report, we describe the Pathogen-Host Interactions database (PHI-base), which systematically compiles such pathogenicity genes involved in pathogen-host interactions. Here, we focus on the biology that underlies this computational resource: the nature of pathogen-host interactions, the experimental methods that exist for the characterization of such pathogen-host interactions as well as the available computational resources. Based on the data, we review and analyze the specific functions of pathogenicity genes, the host-specific nature of pathogenicity and virulence genes, and the generic mechanisms of effectors that trigger plant responses. We further discuss the utilization of PHI-base for the computational identification of pathogenicity genes through comparative genomics. In this context, the importance of standardizing pathogenicity assays as well as integrating databases to aid comparative genomics is discussed.

Download Full-text

Characterization of htrB and msbB Mutants of the Light Organ Symbiont Vibrio fischeri

Applied and Environmental Microbiology ◽

10.1128/aem.02138-07 ◽

2007 ◽

Vol 74 (3) ◽

pp. 633-644 ◽

Cited By ~ 15

Author(s):

Dawn M. Adin ◽

Nancy J. Phillips ◽

Bradford W. Gibson ◽

Michael A. Apicella ◽

Edward G. Ruby ◽

...

Keyword(s):

Lipid A ◽

Vibrio Fischeri ◽

Sodium Dodecyl ◽

Chromosome 1 ◽

Chromosome 2 ◽

Euprymna Scolopes ◽

Host Interactions ◽

Lipid A Structure ◽

Bacterial Lipid

ABSTRACT Bacterial lipid A is an important mediator of bacterium-host interactions, and secondary acylations added by HtrB and MsbB can be critical for colonization and virulence in pathogenic infections. In contrast, Vibrio fischeri lipid A stimulates normal developmental processes in this bacterium's mutualistic host, Euprymna scolopes, although the importance of lipid A structure in this symbiosis is unknown. To further examine V. fischeri lipid A and its symbiotic function, we identified two paralogs of htrB (designated htrB1 and htrB2) and an msbB gene in V. fischeri ES114 and demonstrated that these genes encode lipid A secondary acyltransferases. htrB2 and msbB are found on the Vibrio “housekeeping” chromosome 1 and are conserved in other Vibrio species. Mutations in htrB2 and msbB did not impair symbiotic colonization but resulted in phenotypic alterations in culture, including reduced motility and increased luminescence. These mutations also affected sensitivity to sodium dodecyl sulfate, kanamycin, and polymyxin, consistent with changes in membrane permeability. Conversely, htrB1 is located on the smaller, more variable vibrio chromosome 2, and an htrB1 mutant was wild-type-like in culture but appeared attenuated in initiating the symbiosis and was outcompeted 2.7-fold during colonization when mixed with the parent. These data suggest that htrB2 and msbB play conserved general roles in vibrio biology, whereas htrB1 plays a more symbiosis-specific role in V. fischeri.

Download Full-text

Characterization of two LuxI/R homologs in Pantoea ananatis LMG 2665T

Canadian Journal of Microbiology ◽

10.1139/cjm-2016-0143 ◽

2016 ◽

Vol 62 (11) ◽

pp. 893-903 ◽

Cited By ~ 7

Author(s):

Siphathele Sibanda ◽

Jacques Theron ◽

Divine Y. Shyntum ◽

Lucy N. Moleleki ◽

Teresa A. Coutinho

Keyword(s):

Quorum Sensing ◽

Genome Sequence ◽

Biofilm Formation ◽

Biological Significance ◽

Bacterial Strains ◽

Pantoea Ananatis ◽

Ecological Fitness ◽

Host Interactions

Quorum sensing (QS) plays an important role in the regulation of bacteria–host interactions and ecological fitness in many bacteria. In this study, 2 luxI/R homologs, namely eanI/eanR and rhlI/rhlR, were identified in the genome sequence of Pantoea ananatis LMG 2665T. To determine a role for these luxI/R homologs in pathogenicity and biofilm formation, mutant bacterial strains lacking either eanI/R or rhlI/R and both of these homologs were generated. The results indicated that both the RhlI/R and EanI/R systems are required for pathogenicity and biofilm formation in strain LMG 2665T. This is the first study to characterize the biological significance of the RhlI/R QS system in P. ananatis.

Download Full-text

Characterization of Streptococcus thermophilus Host Range Phage Mutants

Applied and Environmental Microbiology ◽

10.1128/aem.72.4.3036-3041.2006 ◽

2006 ◽

Vol 72 (4) ◽

pp. 3036-3041 ◽

Cited By ~ 32

Author(s):

Martin Duplessis ◽

Céline M. Lévesque ◽

Sylvain Moineau

Keyword(s):

Host Range ◽

Point Mutations ◽

Streptococcus Thermophilus ◽

Structural Proteins ◽

Laser Desorption Ionization ◽

Wild Type ◽

Ionization Time ◽

Host Interactions ◽

Flight Mass Spectrometry

ABSTRACT To investigate phage-host interactions in Streptococcus thermophilus, a phage-resistant derivative (SMQ-301R) was obtained by challenging a Tn917 library of phage-sensitive strain S. thermophilus SMQ-301 with virulent phage DT1. Mutants of phages DT1 and MD2 capable of infecting SMQ-301 and SMQ-301R were isolated at a frequency of 10−6. Four host range phage mutants were analyzed further and compared to the two wild-type phages. Altogether, three genes (orf15, orf17, and orf18) contained point mutations leading to amino acid substitutions and were responsible for the expanded host range. These three proteins were also identified in both phages by N-terminal sequencing and/or matrix-assisted laser desorption ionization-time-of-flight mass spectrometry. The results suggest that at least three phage structural proteins may be involved in phage-host interactions in S. thermophilus.

Download Full-text

A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features

10.1101/2021.02.17.431625 ◽

2021 ◽

Author(s):

Saman Fatihi ◽

Surabhi Rathore ◽

Ankit Pathak ◽

Deepanshi Gahlot ◽

Mitali Mukerji ◽

...

Keyword(s):

Genomic Data ◽

Structural Features ◽

Antigenic Drift ◽

Spike Protein ◽

Wild Type ◽

Genome Sequences ◽

Host Interactions ◽

Rigorous Framework ◽

Dynamics Simulations ◽

Viral Host Interactions

AbstractThe recent release of SARS-CoV-2 genomic data from several countries has provided clues into the potential antigenic drift of the coronavirus population. In particular, the genomic instability observed in the spike protein necessitates immediate action and further exploration in the context of viral-host interactions. Here we dynamically track 3,11,795 genome sequences of spike protein, which comprises 2,584 protein mutations. We reveal mutational genomic ensemble at different timing and geographies, that evolves on four distinct residues. In addition to the well-established N501 mutational cluster, we detect the presence of three novel clusters, namely A222, N439, and S477. The robust examination of structural features from 44 known cryo-EM structures showed that the virus is deploying many mutations within these clusters on structurally heterogeneous regions. One such dominant variant D614G was also simulated using molecular dynamics simulations and, as compared to wild-type, we found higher stability with human ACE2 receptor. There is also a significant overlap of mutational clusters on known epitopes, indicating putative interference with antibody binding. Thus, we propose that the resulting coaxility of mutational clusters is the most efficient feature of SARS-CoV-2 evolution and provides precise mutant combinations that can enable future vaccine re-positioning.

Download Full-text