The maize ALDH protein superfamily: linking structural features to functional specificities

<p>Abstract</p> <p>Background</p> <p>The completion of maize genome sequencing has resulted in the identification of a large number of uncharacterized genes. Gene annotation and functional characterization of gene products are important to uncover novel protein functionality.</p> <p>Results</p> <p>In this paper, we identify, and annotate members of all the maize aldehyde dehydrogenase (ALDH) gene superfamily according to the revised nomenclature criteria developed by ALDH Gene Nomenclature Committee (AGNC). The maize genome contains 24 unique <it>ALDH </it>sequences encoding members of ten ALDH protein families including the previously identified male fertility restoration <it>RF2A </it>gene, which encodes a member of mitochondrial class 2 ALDHs. Using computational modeling analysis we report here the identification, the physico-chemical properties, and the amino acid residue analysis of a novel tunnel like cavity exclusively found in the maize sterility restorer protein, RF2A/ALDH2B2 by which this protein is suggested to bind variably long chain molecular ligands and/or potentially harmful molecules.</p> <p>Conclusions</p> <p>Our finding indicates that maize ALDH superfamily is the most expanded of plant <it>ALDHs </it>ever characterized, and the mitochondrial maize RF2A/ALDH2B2 is the only plant ALDH that harbors a newly defined pocket/cavity with suggested functional specificity.</p

Modeling-Dependent Protein Characterization of the Rice Aldehyde Dehydrogenase (ALDH) Superfamily Reveals Distinct Functional and Structural Features

The completion of the rice genome sequence has made it possible to identify and characterize new genes and to perform comparative genomics studies across taxa. The aldehyde dehydrogenase (ALDH) gene superfamily encoding for NAD(P)+-dependent enzymes is found in all major plant and animal taxa. However, the characterization of plant ALDHs has lagged behind their animal- and prokaryotic-ALDH homologs. In plants, ALDHs are involved in abiotic stress tolerance, male sterility restoration, embryo development and seed viability and maturation. However, there is still no structural property-dependent functional characterization of ALDH protein superfamily in plants. In this paper, we identify members of the rice ALDH gene superfamily and use the evolutionary nesting events of retrotransposons and protein-modeling–based structural reconstitution to report the genetic and molecular and structural features of each member of the rice ALDH superfamily in abiotic/biotic stress responses and developmental processes. Our results indicate that rice-ALDHs are the most expanded plant ALDHs ever characterized. This work represents the first report of specific structural features mediating functionality of the whole families of ALDHs in an organism ever characterized

Abnormally high digestive enzyme activity and gene expression explain the contemporary evolution of a diabrotica biotype able to feed on soybeans

Western corn rootworm (Diabrotica virgifera) (WCR) depends on the continuous availability of corn. Broad adoption of annual crop rotation between corn (Zea mays) and nonhost soybean (Glycine max) exploited WCR biology to provide excellent WCR control, but this practice dramatically reduced landscape heterogeneity in East-central Illinois and imposed intense selection pressure. This selection resulted in behavioral changes and "rotation-resistant" (RR) WCR adults. Although soybeans are well defended against Coleopteran insects by cysteine protease inhibitors, RR-WCR feed on soybean foliage and remain long enough to deposit eggs that will hatch the following spring and larvae will feed on roots of planted corn. Other than documenting changes in insect mobility and egg laying behavior, 15 years of research have failed to identify any diagnostic differences between wild-type (WT)- and RR-WCR or a mechanism that allows for prolonged RR-WCR feeding and survival in soybean fields. We documented differences in behavior, physiology, digestive protease activity (threefold to fourfold increases), and protease gene expression in the gut of RR-WCR adults. Our data suggest that higher constitutive activity levels of cathepsin L are part of the mechanism that enables populations of WCR to circumvent soybean defenses, and thus, crop rotation. These new insights into the mechanism of WCR tolerance of soybean herbivory transcend the issue of RR-WCR diagnostics and management to link changes in insect gut proteolytic activity and behavior with landscape heterogeneity. The RR-WCR illustrates how agroecological factors can affect the evolution of insects in human-altered ecosystems.Fil: Curzi, Matias J.. University of Illinois at Urbana; Estados UnidosFil: Zavala, Jorge Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones en Biociencias Agrícolas y Ambientales. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones en Biociencias Agrícolas y Ambientales; ArgentinaFil: Spencer, Joseph L.. University of Illinois at Urbana; Estados UnidosFil: Seufferheld, Manfredo Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones en Biociencias Agrícolas y Ambientales. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones en Biociencias Agrícolas y Ambientales; Argentin

Halopeptonella vilamensis gen. nov, sp. nov., a halophilic strictly aerobic bacterium of the family Ectothiorhodospiraceae

A Gram-negative, halophilic, heterotrophic, rod-shaped, non-spore-forming bacterium (SV525T) was isolated from the sediment of a hypersaline lake located at 4600 m above sea level (Laguna Vilama, Argentina). Strain SV525T was strictly aerobic and formed pink-to-magenta colonies. Growth occurred at 10–35 °C (optimum 25–30 °C), at pH levels 6.0–8.5 (optimum 7.0) and at NaCl concentrations of 7.5–25 % (w/v) with an optimum at 10–15 % (w/v). The strain required sodium and magnesium but not potassium ions for growth. Grows with tryptone, or Bacto Peptone as sole carbon and energy source and requires yeast extract for growth. It produced catalase and oxidase. The predominant ubiquinone was Q-8 and the major fatty acids comprised C18:1ω7c, C16:0 and C18:0. The DNA G+C content was 60.4 mol% and its polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and a phosphoglycolipid. Phylogenetic analysis based on 16S rRNA gene indicated that strain SV525T belongs to the family Ectothiorhodospiraceae within the class Gammaproteobacteria. On the basis of phylogenetic and phenotypic data, SV525T represents a novel genus and species, for which the name Halopeptonella vilamensis gen. nov., sp. nov. is proposed. The type strain is SV525T (=DSM 21056T =JCM 16388T =NCIMB 14596T).Fil: Menes, Rodolfo Javier. Universidad de la Republica Facultad de Quimica; UruguayFil: Viera, Claudia Elizabeth. Universidad de la Republica Facultad de Quimica; UruguayFil: Farias, Maria Eugenia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Planta Piloto de Procesos Industriales Microbiologicos; ArgentinaFil: Seufferheld, Manfredo Jose. University of Illinois. Urbana - Champaign; Estados Unido

Halomonas vilamensis sp. nov., isolated from high-altitude Andean lakes

A Gram-negative, aerobic, rod-shaped, non-spore-forming bacterium (SV325T) was isolated from the sediment of a hypersaline lake located at 4600 m above sea level (Laguna Vilama, Argentina). Strain SV325T formed cream-to-pink colonies, was motile and moderately halophilic, and grew at NaCl concentrations of 1-25 % (w/v) with an optimum at 5-10 % (w/v). Growth occurred at 5-40 degrees C (optimum around 30 degrees C) and at pH levels 5.0-10.0 (optimum 7.0-8.0). The bacteria does not produce exopolysaccharides, stained positively for intracellular polyphosphate granules but not for poly-beta-hydroxyalkanoates It produced catalase and oxidase, reduced nitrate to nitrite, hydrolyzed gelatin, did not produce acids from sugars, and utilized a limited range of substrates as carbon and energy sources: acetate, caproate, fumarate, DL-beta-hydroxybutyrate, malate, maleate, malonate and succinate. The predominant ubiquinones were Q-9 (92.5 %) and Q-8 (7.5 %), the major fatty acids were C19:0 cyclo omega8c, C16:0, C17:0 cyclo and C16:1 omega7c/15 iso 2-OH, and the DNA G+C content was 55.0 mol%. Phylogenetic analyses based on 16S rRNA gene indicated that strain SV325T belongs to the genus Halomonas in the class Gammaproteobacteria. Physiological and biochemical tests allowed phenotypic differentiation of strain SV325T from closely related, valid, published species names and therefore represents a new species; the name Halomonas vilamensis sp. nov. is proposed for this species, with type strain SV325T (=DSM 21020T =LMG 24332T).Fil: Menes, Rodolfo Javier. Universidad de la Republica. Facultad de Química y Facultad de Ciencias; UruguayFil: Viera, Claudia Elizabeth. Universidad de la Republica. Facultad de Química y Facultad de Ciencias; UruguayFil: Farias, Maria Eugenia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Tucumán. Planta Piloto de Procesos Industriales Microbiológicos (i); ArgentinaFil: Seufferheld, Manfredo Jose. University Of Illinois At Urbana; Estados Unido

Gut bacteria facilitate adaptation to crop rotation in the western corn rootworm

Insects are constantly adapting to human-driven landscape changes; however, the roles of their gut microbiota in these processes remain largely unknown. The western corn rootworm (WCR, Diabrotica virgifera virgifera LeConte) (Coleoptera: Chrysomelidae) is amajor corn pest that has been controlled via annual rotation between corn (Zea mays) and nonhost soybean (Glycine max) in the United States. This practice selected for a ?rotation-resistant? variant (RR-WCR) with reduced ovipositional fidelity to cornfields.When in soybean fields, RRWCRs also exhibit an elevated tolerance of antiherbivory defenses (i.e., cysteine protease inhibitors) expressed in soybean foliage. Here we show that gut bacterial microbiota is an important factor facilitating this corn specialist?s (WCR?s) physiological adaptation to brief soybean herbivory. Comparisons of gut microbiota between RR- and wild-type WCR (WT-WCR) revealed concomitant shifts in bacterial community structure with host adaptation to soybean diets. Antibiotic suppression of gut bacteria significantly reduced RR-WCR tolerance of soybean herbivory to the level of WT-WCR, whereas WTWCR were unaffected. Our findings demonstrate that gut bacteria help to facilitate rapid adaptation of insects inmanaged ecosystems.Fil: Chu, C. C.. University Of Illinois; Estados Unidos de América;Fil: Spencer, J.. University Of Illinois; Estados Unidos de América;Fil: Curzi, M.. University Of Illinois; Estados Unidos de América;Fil: Zavala, Jorge Alberto. Universidad de Buenos Aires. Facultad de Agronomia;Fil: Seufferheld, Manfredo Jose. University Of Illinois; Estados Unidos de América

Patterns of differential gene expression in adult rotation-resistant and wild-type western corn rootworm digestive tracts

The western corn rootworm (WCR, Diabrotica virgifera virgifera LeConte) is an important pest of corn. Annual crop rotation between corn and soybean disrupts the corn‐dependent WCR life cycle and is widely adopted to manage this pest. This strategy selected for rotation‐resistant (RR) WCR with reduced ovipositional fidelity to corn. Previous studies revealed that RR‐WCR adults exhibit greater tolerance of soybean diets, different gut physiology, and host–microbe interactions compared to rotation‐susceptible wild types (WT). To identify the genetic mechanisms underlying these phenotypic changes, a de novo assembly of the WCR adult gut transcriptome was constructed and used for RNA‐sequencing analyses of RNA libraries from different WCR phenotypes fed with corn or soybean diets. Global gene expression profiles of WT‐ and RR‐WCR were similar when feeding on corn diets, but different when feeding on soybean. Using network‐based methods, we identified gene modules transcriptionally correlated with the RR phenotype. Gene ontology enrichment analyses indicated that the functions of these modules were related to metabolic processes, immune responses, biological adhesion, and other functions/processes that appear to correlate to documented traits in RR populations. These results suggest that gut transcriptomic divergence correlated with brief soybean feeding and other physiological traits may exist between RR‐ and WT‐WCR adults.Fil: Chu, Chia-Ching. University of Illinois at Urbana; Estados UnidosFil: Zavala, Jorge Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Agronomía; ArgentinaFil: Spencer, Joseph L.. University of Illinois; Estados UnidosFil: Curzi, Matías J.. DuPont Pioneer; ArgentinaFil: Fields, Christopher J.. Biotechnology Center; Estados UnidosFil: Drnevich, Jenny. Biotechnology Center; Estados UnidosFil: Siegfried, Blair D.. Universidad de Nebraska - Lincoln; Estados UnidosFil: Seufferheld, Manfredo Jose. University of Illinois at Urbana; Estados Unidos. University of Illinois; Estados Unido