HighlightMaize primary root tissues display extensive transcriptomic plasticity upon water deficit. The most significant adaptive changes in the elongation zone lead to reprogramming of metabolism and cell wall organization.

HighlightTranscriptomic and anatomical analyses of primary, seminal, and crown roots of the maize inbred line B73 revealed root type-specific diversity related to the different functions of these root types during development.

Maize (Zea mays L.) displays an exceptional degree of structural genomic diversity [1, 2]. In addition, variation in gene expression further contributes to the extraordinary phenotypic diversity and plasticity of maize. This study provides a systematic investigation on how distantly related homozygous maize inbred lines affect the transcriptomic plasticity of their highly heterozygous F hybrids. The classical dominance model of heterosis explains the superiority of hybrid plants by the complementation of deleterious parental alleles by superior alleles of the second parent at many loci [3]. Genes active in one inbred line but inactive in another represent an extreme instance of allelic diversity defined as single-parent expression [4]. We observed on average ∼1,000 such genes in all inbred line combinations during primary root development. These genes consistently displayed expression complementation (i.e., activity) in their hybrid progeny. Consequently, extreme expression complementation is a general mechanism that results on average in ∼600 additionally active genes and their encoded biological functions in hybrids. The modern maize genome is complemented by a set of non-syntenic genes, which emerged after the separation of the maize and sorghum lineages and lack syntenic orthologs in any other grass species [5]. We demonstrated that non-syntenic genes are the driving force of gene expression complementation in hybrids. Among those, the highly diversified families of bZIP and bHLH transcription factors [6] are systematically overrepresented. In summary, extreme gene expression complementation extensively shapes the transcriptomic plasticity of maize hybrids and might therefore be one factor controlling the developmental plasticity of hybrids.

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f Avian pathogenic Escherichia coli (APEC) strains cause one of the three most significant infectious diseases in the poultry industry and are also potential food-borne pathogens threating human health. In this study, we showed that ArcA (aerobic respiratory control), a global regulator important for E. coli's adaptation from anaerobic to aerobic conditions and control of that bacterium's enzymatic defenses against reactive oxygen species (ROS), is involved in the virulence of APEC. Deletion of arcA significantly attenuates the virulence of APEC in the duck model. Transcriptome sequencing (RNA-Seq) analyses comparing the APEC wild type and the arcA mutant indicate that ArcA regulates the expression of 129 genes, including genes involved in citrate transport and metabolism, flagellum synthesis, and chemotaxis. Further investigations revealed that citCEFXG contributed to APEC's microaerobic growth at the lag and log phases when cultured in duck serum and that ArcA played a dual role in the control of citrate metabolism and transportation. In addition, deletion of flagellar genes motA and motB and chemotaxis gene cheA significantly attenuated the virulence of APEC, and ArcA was shown to directly regulate the expression of motA, motB, and cheA. The combined results indicate that ArcA controls metabolism, chemotaxis, and motility contributing to the pathogenicity of APEC. Commensal and pathogenic Escherichia coli strains can grow under both aerobic and anaerobic conditions. The enzymes required for catabolism under aerobic versus anaerobic conditions are substantially different, and E. coli has the ability to switch among anaerobic, anaerobic respiratory, and fermentative pathways (1). The expression of genes involved in cellular functions such as nutrient uptake and/or excretion systems, biosynthetic pathways, and macromolecular synthesis are also adjusted in response to oxygen availability (2). The Arc two-component signal transduction system, comprised of the kinase sensor ArcB and its cognate response regulator ArcA, is one of the mechanisms that enable E. coli adaptation to changing oxygen availability (3). Once an environmental signal is received, ArcB undergoes autophosphorylation and catalyzes the transphosphorylation of ArcA, which then promotes or represses expression of Arc-regulated genes. Rather than directly detecting environmental O 2 , ArcB probably senses the redox state of the cell through detection of a reduced electron transport component (4). Under aerobic conditions (5), oxidized forms of quinone electron carriers in the membrane inhibit the autophosphorylation of ArcB, while under anaerobic and microaerobic conditions, ArcB undergoes autophosphorylation. The net activity of ArcB as a kinase for ArcA is expected to progressively increase during the transition from aerobic to anaerobic growth.The ArcA regulon of E. coli K-12 strains has been extensively studied under both aerobic and anaerobic conditions (6, 7). A previous study indicated that about 1,139 genes in the E. coli K-12 genome are regu...