Over the years, IGBB scientists have gained a reputation for publishing papers that are widely cited. Information regarding the 100 most highly cited papers authored/co-authored by IGBB employees, faculty fellows, and affiliates is presented below. Citation values are from Scopus. For a particular IGBB fellow/affiliate/staff member, only those papers published while at MS State are included.
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The histone methyltransferase SDG8 regulates shoot branching in Arabidopsis
Dong G, Ma DP,Li J (2008) The histone methyltransferase SDG8 regulates shoot branching in Arabidopsis. Biochemical and Biophysical Research Communications 373(4): 659-64.
ABSTRACT Histone lysine methylation is an evolutionally conserved modification involved in determining chromatin states associated with gene activation or repression. Here we report that the Arabidopsis SET domain group 8 (SDG8) protein is a histone H3 methyltransferase involved in regulating shoot branching. Knockout mutations of the SDG8 gene markedly reduce the global levels of histone H3 trimethylation at lysines 9 and 36 as well as dimethylation at lysine 36. The sdg8 mutants produce more shoot branches than wild-type plants. The expression of SPS/BUS (supershoot/bushy), a repressor of shoot branching, is decreased in sdg8 mutants, while UGT74E2 (UDP-glycosyltransferase 74E2), a gene associated with increased shoot branching, is up-regulated in sdg8 mutants. The altered expression of SPS/BUS and UGT74E2 correlates with changed histone H3 methylation at these loci. These results suggest that SDG8 regulates shoot branching via controlling the methylation states of its target genes.
Global analysis of lysine acetylation suggests the involvement of protein acetylation in diverse biological processes in rice (Oryza sativa)
IGBB Authors: Babi R.R. Nallamilli, Mariola J. Edelmann, Hana Mujahid, Zhaohua Peng
Nallamilli BR, Edelmann MJ, Zhong X, Tan F, Mujahid H, Zhang J, Nanduri B, Peng Z (2014) Global analysis of lysine acetylation suggests the involvement of protein acetylation in diverse biological processes in rice (Oryza sativa). PLoS One 9(2): e89283.
ABSTRACT Lysine acetylation is a reversible, dynamic protein modification regulated by lysine acetyltransferases and deacetylases. Recent advances in high-throughput proteomics have greatly contributed to the success of global analysis of lysine acetylation. A large number of proteins of diverse biological functions have been shown to be acetylated in several reports in human cells, E.coli, and dicot plants. However, the extent of lysine acetylation in non-histone proteins remains largely unknown in monocots, particularly in the cereal crops. Here we report the mass spectrometric examination of lysine acetylation in rice (Oryza sativa). We identified 60 lysine acetylated sites on 44 proteins of diverse biological functions. Immunoblot studies further validated the presence of a large number of acetylated non-histone proteins. Examination of the amino acid composition revealed substantial amino acid bias around the acetylation sites and the amino acid preference is conserved among different organisms. Gene ontology analysis demonstrates that lysine acetylation occurs in diverse cytoplasmic, chloroplast and mitochondrial proteins in addition to the histone modifications. Our results suggest that lysine acetylation might constitute a regulatory mechanism for many proteins, including both histones and non-histone proteins of diverse biological functions.
Species formation by host shifting in avian malaria parasites
Ricklefs RE, Outlaw DC, Svensson-Coelho M, Medeiros MC, Ellis VA, Latta S (2014) Species formation by host shifting in avian malaria parasites. Proceedings of the National Academy of Sciences of the United States of America 111(41): 14816-14821.
ABSTRACT The malaria parasites (Apicomplexa: Haemosporida) of birds are believed to have diversified across the avian host phylogeny well after the origin of most major host lineages. Although many symbionts with direct transmission codiversify with their hosts, mechanisms of species formation in vector-borne parasites, including the role of host shifting, are poorly understood. Here, we examine the hosts of sister lineages in a phylogeny of 181 putative species of malaria parasites of New World terrestrial birds to determine the role of shifts between host taxa in the formation of new parasite species. We find that host shifting, often across host genera and families, is the rule. Sympatric speciation by host shifting would require local reproductive isolation as a prerequisite to divergent selection, but this mechanism is not supported by the generalized host-biting behavior of most vectors of avian malaria parasites. Instead, the geographic distribution of individual parasite lineages in diverse hosts suggests that species formation is predominantly allopatric and involves host expansion followed by local host-pathogen coevolution and secondary sympatry, resulting in local shifting of parasite lineages across hosts
Proteome and phosphoproteome analysis of chromatin associated proteins in rice (Oryza sativa)
Tan F, Li G, Chitteti BR, Peng Z (2007) Proteome and phosphoproteome analysis of chromatin associated proteins in rice (Oryza sativa). Proteomics 7(24): 4511-4527.
ABSTRACT The eukaryotic chromatin/chromosome stores genomic information, controls genetic material distribution, and plays an essential role in the establishment and maintenance of spatial and temporal gene expression profile. Despite over a century of research, the protein composition and higher level structure of chromatin still remain obscure, particularly in plants. In this report, we have developed a protocol for chromatin purification from rice suspension cells and examined proteins copurified with chromatin using both 2-DE gel and shotgun approaches. Nine hundred seventy-two distinct protein spots have been resolved on 2-DE gels and 509 proteins have been identified by MALDI-MS/MS following gel excision, which correspond to 269 unique proteins. When the chromatin copurified proteins are examined using shotgun method, a large number of histone variants in addition to the four common core histones have been identified. Other proteins identified include nucleosome assembly proteins, high mobility group proteins, histone modification proteins, transcription factors, and a large number of hypothetical and function unknown proteins. Furthermore, putative phosphoproteins copurified with chromatin have been examined using Pro-Q Diamond phosphoprotein stain and followed by MALDI-MS/MS. Our studies have provided valued new insight into chromatin composition in plants.
Prediction of peptides observable by mass spectrometry applied at the experimental set level
IGBB Authors: William S. Sanders, Susan M. Bridges, Fiona M. McCarthy, Bindu Nanduri, Shane C. Burgess
Sanders WS, Bridges SM, McCarthy FM, Nanduri B, Burgess SC (2007) Prediction of peptides observable by mass spectrometry applied at the experimental set level. BMC Bioinformatics 8(Suppl 7): S23.
ABSTRACT BACKGROUND: When proteins are subjected to proteolytic digestion and analyzed by mass spectrometry using a method such as 2D LC MS/MS, only a portion of the proteotypic peptides associated with each protein will be observed. The ability to predict which peptides can and cannot potentially be observed for a particular experimental dataset has several important applications in proteomics research including calculation of peptide coverage in terms of potentially detectable peptides, systems biology analysis of data sets, and protein quantification. RESULTS: We have developed a methodology for constructing artificial neural networks that can be used to predict which peptides are potentially observable for a given set of experimental, instrumental, and analytical conditions for 2D LC MS/MS (a.k.a Multidimensional Protein Identification Technology [MudPIT]) datasets. Neural network classifiers constructed using this procedure for two MudPIT datasets exhibit 10-fold cross validation accuracy of about 80%. We show that a classifier constructed for one dataset has poor predictive performance with the other dataset, thus demonstrating the need for dataset specific classifiers. Classification results with each dataset are used to compute informative percent amino acid coverage statistics for each protein in terms of the predicted detectable peptides in addition to the percent coverage of the complete sequence. We also demonstrate the utility of predicted peptide observability for systems analysis to help determine if proteins that were expected but not observed generate sufficient peptides for detection. CONCLUSION: Classifiers that accurately predict the likelihood of detecting proteotypic peptides by mass spectrometry provide proteomics researchers with powerful new approaches for data analysis. We demonstrate that the procedure we have developed for building a classifier based on an individual experimental data set results in classifiers with accuracy comparable to those reported in the literature based on large training sets collected from multiple experiments. Our approach allows the researcher to construct a classifier that is specific for the experimental, instrument, and analytical conditions of a single experiment and amenable to local, condition-specific, implementation. The resulting classifiers have application in a number of areas such as determination of peptide coverage for protein identification, pathway analysis, and protein quantification.
Rerooting the evolutionary tree of malaria parasites
Outlaw DC, Ricklefs RE (2011) Rerooting the evolutionary tree of malaria parasites. Proceedings of the National Academy of Sciences of the United States of America 108(32): 13183-13187.
ABSTRACT Malaria parasites (Plasmodium spp.) have plagued humans for millennia. Less well known are related parasites (Haemosporida), with diverse life cycles and dipteran vectors that infect other vertebrates. Understanding the evolution of parasite life histories, including switches between hosts and vectors, depends on knowledge of evolutionary relationships among parasite lineages. In particular, inferences concerning time of origin and trait evolution require correct placement of the root of the evolutionary tree. Phylogenetic reconstructions of the diversification of malaria parasites from DNA sequences have suffered from uncertainty concerning outgroup taxa, limited taxon sampling, and selection on genes used to assess relationships. As a result, inferred relationships among the Haemosporida have been unstable, and questions concerning evolutionary diversification and host switching remain unanswered. A recent phylogeny placed mammalian malaria parasites, as well as avian/reptilian Plasmodium, in a derived position relative to the avian parasite genera Leucocytozoon and Haemoproteus, implying that the ancestral forms lacked merogony in the blood and that their vectors were non-mosquito dipterans. Bayesian, outgroup-free phylogenetic reconstruction using relaxed molecular clocks with uncorrelated rates instead suggested that mammalian and avian/reptilian Plasmodium parasites, spread by mosquito vectors, are ancestral sister taxa, from which a variety of specialized parasite lineages with modified life histories have evolved.
Androglobin: a Chimeric Globin in Metazoans that is Preferentially Expressed in Mammalian Testes
ABSTRACT Comparative genomic studies have led to the recent identification of several novel globin types in Metazoa. They have revealed a surprising evolutionary diversity of functions beyond the familiar O(2) supply roles of hemoglobin and myoglobin. Here we report the discovery of a hitherto unrecognized family of proteins with a unique modular architecture, possessing an N-terminal calpain-like domain, an internal, circular permuted globin domain and an IQ calmodulin-binding motif. Putative orthologs are present in the genomes of many metazoan taxa, including vertebrates. The calpain-like region is homologous to the catalytic domain II of the large subunit of human calpain-7. The globin domain satisfies the criteria of a myoglobin-like fold, but is rearranged and split into two parts. The recombinantly expressed human globin domain exhibits an absorption spectrum characteristic of hexacoordination of the heme iron atom. Molecular evolutionary analyses indicate that this chimeric globin family is phylogenetically ancient and originated in the common ancestor to animals and choanoflagellates. In humans and mice, the gene is predominantly expressed in testis tissue, and we propose the name "androglobin" (Adgb). Expression is associated with postmeiotic stages of spermatogenesis and is insensitive to experimental hypoxia. Evidence exists for increased gene expression in fertile compared to infertile males.
CattleTickBase: An integrated Internet-based bioinformatics resource for Rhipicephalus (Boophilus) microplus
Bellgard MI, Moolhuijzen PM, Guerrero FD, Schibeci D, Rodriguez-Valle M, Peterson DG, Dowd SE, Barrero R, Hunter A, Miller RJ, Lew-Tabor AE (2012) CattleTickBase: An integrated Internet-based bioinformatics resource for Rhipicephalus (Boophilus) microplus. International Journal for Parasitology 42(2): 161-169.
ABSTRACT The Rhipicephalus microplus genome is large and complex in structure, making it difficult to assemble a genome sequence and costly to resource the required bioinformatics. In light of this, a consortium of international collaborators was formed to pool resources to begin sequencing this genome. We have acquired and assembled genomic DNA into contigs that represent over 1.8Gigabase pairs of DNA from gene-enriched regions of the R. microplus genome. We also have several datasets containing transcript sequences from a number of gene expression experiments conducted by the consortium. A web-based resource was developed to enable the scientific community to access our datasets and conduct analysis through a web-based bioinformatics environment called YABI. The collective bioinformatics resource is termed CattleTickBase. Our consortium has acquired genomic and transcriptomic sequence data at approximately 0.9X coverage of the gene-coding regions of the R. microplus genome. The YABI tool will facilitate access and manipulation of cattle tick genome sequence data as the genome sequencing of R. microplus proceeds. During this process the CattleTickBase resource will continue to be updated.
The remarkable evolutionary history of endornaviruses
Roossinck MJ, Sabanadzovic S, Okada R, Valverde RA (2011) The remarkable evolutionary history of endornaviruses. Journal of General Virology 92(Pt 11): 2674-2678.
ABSTRACT The family Endornaviridae contains several members from diverse hosts, including plants, fungi and oomycetes. They are found as large dsRNA elements with a nick in the coding strand. All members encode a conserved RNA-dependent RNA polymerase, but no other domain that is conserved among all members. Based on the conserved domain database comparison the various domains have different origins, indicating a highly modular evolutionary history. In some cases, domains with similar putative functions are found that are derived from different protein families, indicating convergent evolution for a required function.
Molecular basis for broad neuraminidase immunity: Conserved epitopes in seasonal and pandemic H1N1 as well as H5N1 influenza viruses
Wan H, Gao J, Xu K, Chen H, Couzens LK, Rivers KH, Easterbrook JD, Yang K, Zhong L, Rajabi M, Ye J, Sultana I, Wan XF, Liu X, Perez DR, Taubenberger JK, Eichelberger MC (2013) Molecular basis for broad neuraminidase immunity: Conserved epitopes in seasonal and pandemic H1N1 as well as H5N1 influenza viruses. Journal of Virology 87(16): 9290-9300.
ABSTRACT Influenza A viruses, including H1N1 and H5N1 subtypes, pose a serious threat to public health. Neuraminidase (NA)-related immunity contributes to protection against influenza virus infection. Antibodies to the N1 subtype provide protection against homologous and heterologous H1N1 as well as H5N1 virus challenge. Since neither the strain-specific nor conserved epitopes of N1 have been identified, we generated a panel of mouse monoclonal antibodies (MAbs) that exhibit different reactivity spectra with H1N1 and H5N1 viruses and used these MAbs to map N1 antigenic domains. We identified 12 amino acids essential for MAb binding to the NA of a recent seasonal H1N1 virus, A/Brisbane/59/2007. Of these, residues 248, 249, 250, 341, and 343 are recognized by strain-specific group A MAbs, while residues 273, 338, and 339 are within conserved epitope(s), which allows cross-reactive group B MAbs to bind the NAs of seasonal H1N1 and the 1918 and 2009 pandemic (09pdm) H1N1 as well as H5N1 viruses. A single dose of group B MAbs administered prophylactically fully protected mice against lethal challenge with seasonal and 09pdm H1N1 viruses and resulted in significant protection against the highly pathogenic wild-type H5N1 virus. Another three N1 residues (at positions 396, 397, and 456) are essential for binding of cross-reactive group E MAbs, which differ from group B MAbs in that they do not bind 09pdm H1N1 viruses. The identification of conserved N1 epitopes reveals the molecular basis for NA-mediated immunity between H1N1 and H5N1 viruses and demonstrates the potential for developing broadly protective NA-specific antibody treatments for influenza.
Bacteriophage significantly reduces Listeria monocytogenes on raw salmon fillet tissue
Soni KA, Nannapaneni R (2010) Bacteriophage significantly reduces Listeria monocytogenes on raw salmon fillet tissue. Journal of Food Protection 73(1): 32-38.
ABSTRACT We have demonstrated the antilisterial activity of generally recognized as safe (GRAS) bacteriophage LISTEX P100 (phage P100) on the surface of raw salmon fillet tissue against Listeria monocytogenes serotypes 1/2a and 4b. In a broth model system, phage P100 completely inhibited L. monocytogenes growth at 4 degrees Celsius for 12 days, at 10 degrees Celsius for 8 days, and at 30 degrees Celsius for 4 days, at all three phage concentrations of 10(4), 10(6), and 10(8) PFU/ml. On raw salmon fillet tissue, a higher phage concentration of 10(8) PFU/g was required to yield 1.8-, 2.5-, and 3.5-log CFU/g reductions of L. monocytogenes from its initial loads of 2, 3, and 4.5 log CFU/g at 4 or 22 degrees Celsius. Over the 10 days of storage at 4 degrees Celsius, L. monocytogenes growth was inhibited by phage P100 on the raw salmon fillet tissue to as low as 0.3 log CFU/g versus normal growth of 2.6 log CFU/g in the absence of phage. Phage P100 remained stable on the raw salmon fillet tissue over a 10-day storage period, with only a marginal loss of 0.6 log PFU/g from an initial phage treatment of 8 log PFU/g. These findings illustrate that the GRAS bacteriophage LISTEX P100 is listericidal on raw salmon fillets and is useful in quantitatively reducing L. monocytogenes.
Southern tomato virus: The link between the families Totiviridae and Partitiviridae
Sabanadzovic S, Valverde RA, Brown JK, Martin RR, Tzanetakis IE (2009) Southern tomato virus: The link between the families Totiviridae and Partitiviridae. Virus Research 140(1-2): 130-137.
ABSTRACT A dsRNA virus with a genome of 3.5 kb was isolated from field and greenhouse-grown tomato plants of different cultivars and geographic locations in North America. Cloning and sequencing of the viral genome showed the presence of two partially overlapping open reading frames (ORFs), and a genomic organization resembling members of the family Totiviridae that comprises fungal and protozoan viruses, but not plant viruses. The 5'-proximal ORF codes for a 377 amino acid-long protein of unknown function, whereas the product of ORF2 contains typical motifs of an RNA-dependant RNA-polymerase and is likely expressed by a +1 ribosomal frame shift. Despite the similarity in the genome organization with members of the family Totiviridae, this virus shared very limited sequence homology with known totiviruses or with other viruses. Repeated attempts to detect the presence of an endophytic fungus as the possible host of the virus failed, supporting its phytoviral nature. The virus was efficiently transmitted by seed but not mechanically and/or by grafting. Phylogenetic analyses revealed that this virus, for which the name Southern tomato virus (STV) is proposed, belongs to a partitivirus-like lineage and represents a species of a new taxon of plant viruses.
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