Nicole A. Grieshaber

Chlamydia trachomatis uses host cell dynein to traffic to the microtubule-organizing center in a p50 dynamitin-independent process

Chlamydiae are pathogenic obligate intracellular bacteria with a biphasic developmental cycle that involves cell types adapted for extracellular survival (elementary bodies, EBs) and intracellular multiplication (reticulate bodies, RBs). The intracellular development of chlamydiae occurs entirely within a membrane-bound vacuole termed an inclusion. Within 2 hours after entry into host cells, Chlamydia trachomatis EBs are trafficked to the perinuclear region of the host cell and remain in close proximity to the Golgi apparatus, where they begin to fuse with a subset of host vesicles containing sphingomyelin. Here, we provide evidence that chlamydial migration from the cell periphery to the peri-Golgi region resembles host cell vesicular trafficking. Chlamydiae move towards the minus end of microtubules and aggregate at the microtubule-organizing center (MTOC). In mammalian cells the most important minus-end-directed microtubule motor is cytoplasmic dynein. Microinjection of antibodies to a subunit of cytoplasmic dynein inhibited movement of chlamydiae to the MTOC, whereas microinjection of antibodies to the plus-directed microtubule motor, kinesin, had no effect. Surprisingly, overexpression of the protein p50 dynamitin, a subunit of the dynactin complex that links vesicular cargo to the dynein motor in minus directed vesicle trafficking, did not abrogate chlamydial migration even though host vesicle transport was inhibited. Nascent chlamydial inclusions did, however, colocalize with the p150(Glued) dynactin subunit, which suggests that p150(Glued) may be required for dynein activation or processivity but that the cargo-binding activity of dynactin, supplied by p50 dynamitin subunits and possibly other subunits, is not. Because chlamydial transcription and translation were required for this intracellular trafficking, chlamydial proteins modifying the cytoplasmic face of the inclusion membrane are probable candidates for proteins fulfilling this function.

A small RNA inhibits translation of the histone-like protein Hc1 in Chlamydia trachomatis

The chromatin of chlamydial elementary bodies (EBs) is stabilized by proteins with sequence homology to eukaryotic H1. These histone homologues, termed Hc1 and Hc2, are expressed only during the late stages of the chlamydial life cycle concomitant with the reorganization of reticulate bodies (RBs) into metabolically inactive EBs. Hc1 and Hc2 play a major role in establishment of nucleoid structure as well as in downregulation of gene expression as RBs differentiate back to EBs. The effects of Hc1 on gene expression patterns requires that chlamydiae strictly control Hc1 activity. Hc1 expression and activity are thus regulated transcriptionally as well as post‐transcriptionally. We describe here a small regulatory RNA (sRNA) that acts as an additional checkpoint to negatively regulate Hc1 synthesis. Coexpression of the sRNA with hctA, the gene that encodes Hc1, in Escherichia coli inhibited Hc1 translation but did not affect hctA mRNA transcription or stability. IhtA (inhibitor of hctA translation) was present only in purified RBs while Hc1 was present only in purified EBs. During infection IhtA, but not Hc1, was present in RBs and was downregulated while Hc1 was upregulated upon RB to EB differentiation. Thus, we propose that IhtA is part of a global regulatory circuit that controls differentiation of RBs to EBs during the chlamydial life cycle.

Chlamydia trachomatis causes centrosomal defects resulting in chromosomal segregation abnormalities.

Chlamydiae traffic along microtubules to the microtubule organizing center (MTOC) to establish an intracellular niche within the host cell. Trafficking to the MTOC is dynein dependent although the activating and cargo‐linking function of the dynactin complex is supplanted by unknown chlamydial protein(s). We demonstrate that once localized to the MTOC, the chlamydial inclusion maintains a tight association with cellular centrosomes. This association is sustained through mitosis and leads to a significant increase in supernumerary centrosomes, abnormal spindle poles, and chromosomal segregation defects. Chlamydial infection thus can lead to chromosome instability in cells that recover from infection.

Regulation of the Chlamydia trachomatis Histone H1-Like Protein Hc2 Is IspE Dependent and IhtA Independent

The chlamydial histone-like proteins, Hc1 and Hc2, function as global regulators of chromatin structure and gene expression. Hc1 and Hc2 expression and activity are developmentally regulated. A small metabolite that disrupts Hc1 interaction with DNA also disrupts Hc2 interactions; however, the small regulatory RNA that inhibits Hc1 translation is specific to Hc1.

Novel Embryonic Genes Are Preferentially Expressed by Autonomously Replicating Rat Embryonic and Neointimal Smooth Muscle Cells

We sought to identify and characterize the expression pattern of genes expressed by smooth muscle cells (SMCs) during periods of self-driven replication during vascular development and after vascular injury. Primary screening of a rat embryonic aortic SMC–specific cDNA library was accomplished with an autonomous embryonic SMC–enriched, nonautonomous adult SMC–subtracted cDNA probe. Positive clones were rescreened in parallel with embryonic SMC–specific and adult SMC–specific cDNA probes. We identified 14 clones that hybridized only with the embryonic cDNA (“emb” clones), 11 of which did not share significant homology with sequences in any of the databases. Five of these novel emb genes (emb7, emb8, emb20, emb37, and emb41) were selectively and only transiently reexpressed in vivo by neointimal SMCs during periods of rapid replication. The emb8:embryonic growth–associated protein (EGAP), which was studied the most extensively, was expressed at high levels by cultured, autonomously replicating embryonic and neointimal SMCs but was detected only at low levels even in mitogenically stimulated adult SMCs. Finally, the administration of antisense EGAP oligonucleotides markedly attenuated embryonic and neointimal SMC replication rates. We suggest that autonomous replication of SMCs may be essential for normal vascular morphogenesis and for the vascular response to injury and that these newly identified “embryonic” genes may be part of the molecular machinery that drives this unique growth phenotype.

Expression of Porphyromonas gingivalis small RNA in response to hemin availability identified using microarray and RNA-seq analysis

There is a significant body of work suggesting that sRNA-mediated post-transcriptional regulation is a conserved mechanism among pathogenic bacteria to modulate bacterial virulence and survival. Porphyromonas gingivalis is recognized as an etiological agent of periodontitis and implicated in contributing to the development of multiple inflammatory diseases including cardiovascular disease. Using NimbleGen microarray analysis and a strand-specific method to sequence cDNA libraries of small RNA-enriched P. gingivalis transcripts using Illuminas high-throughput sequencing technology, we identified putative sRNA and generated sRNA expression profiles in response to growth phase, hemin availability after hemin starvation, or both. We identified transcripts that mapped to intergenic sequences as well as antisense transcripts that mapped to open reading frames of the annotated genome. Overall, this approach provided a comprehensive way to survey transcriptional activity to discover functionally linked RNA transcripts, responding to specific environmental cues, that merit further investigation.

Translation Inhibition of the Developmental Cycle Protein HctA by the Small RNA IhtA Is Conserved across Chlamydia

The developmental cycle of the obligate intracellular pathogen Chlamydia trachomatis serovar L2 is controlled in part by the small non-coding RNA (sRNA), IhtA. All Chlamydia alternate in a regulated fashion between the infectious elementary body (EB) and the replicative reticulate body (RB) which asynchronously re-differentiates back to the terminal EB form at the end of the cycle. The histone like protein HctA is central to RB:EB differentiation late in the cycle as it binds to and occludes the genome, thereby repressing transcription and translation. The sRNA IhtA is a critical component of this regulatory loop as it represses translation of hctA until late in infection at which point IhtA transcription decreases, allowing HctA expression to occur and RB to EB differentiation to proceed. It has been reported that IhtA is expressed during infection by the human pathogens C. trachomatis serovars L2, D and L2b and C. pneumoniae. We show in this work that IhtA is also expressed by the animal pathogens C. caviae and C. muridarum. Expression of HctA in E. coli is lethal and co-expression of IhtA relieves this phenotype. To determine if regulation of HctA by IhtA is a conserved mechanism across pathogenic chlamydial species, we cloned hctA and ihtA from C. trachomatis serovar D, C. muridarum, C. caviae and C. pneumoniae and assayed for rescue of growth repression in E. coli co-expression studies. In each case, co-expression of ihtA with the cognate hctA resulted in relief of growth repression. In addition, expression of each chlamydial species IhtA rescued the lethal phenotype of C. trachomatis serovar L2 HctA expression. As biolayer interferometry studies indicate that IhtA interacts directly with hctA message for all species tested, we predict that conserved sequences of IhtA are necessary for function and/or binding.

Identification of the base-pairing requirements for repression of hctA translation by the small RNA IhtA leads to the discovery of a new mRNA target in Chlamydia trachomatis.

The non-coding small RNA, IhtA expressed by the obligate intracellular human pathogen Chlamydia trachomatis modulates the translation of HctA, a key protein involved in replicative to infectious cell type differentiation. Using a combination of bioinformatics and mutagenesis we sought to identify the base pairing requirement for functional repression of HctA protein expression, with an eye to applying our findings towards the identification of additional targets. IhtA is predicted to fold into a three stem:loop structure. We found that loop 1 occludes the initiation codon of hctA, while loop 2 and 3 are not required for function. This 7 nucleotide region forms G/C rich interactions surrounding the AUG of hctA. Two additional genes in the chlamydial genome, CTL0322 and CTL0097, contained some elements of the hctA:IhtA recognition sequence. The mRNA of both CTL0322and CTL0097 interacted with IhtA in vitro as measured by biolayer interferometry. However, using a CheZ reporter expression system, IhtA only inhibited the translation of CTL0322. The proposed IhtA recognition site in the CTL0322 message contains significant G/C base pairing on either side of the initiation codon while CTL0097 only contains G/C base pairing 3’ to the AUG initiation codon. These data suggest that as the functional interacting region is only 6-7nt in length that full translation repression is dependent on the degree of G/C base pairing. Additionally our results indicate that IhtA may regulate multiple mRNAs involved in the chlamydial infectious cycle.

The role of the chlamydial effector CPAF in the induction of genomic instability

The role of CPAF in chlamydial virulence is justifiably a tangle of confusion. CPAF is a potent and promiscuous cysteine protease capable of cleaving many proteins (Zhong, 2011). Over the 13 years since the original characterization of CPAF in the laboratory of Guaming Zohng (Zhong et al ., 2001) chlamydial researchers have contributed a long list of identified CPAF cleavable target proteins of both chlamydial and host origin (A Conrad et al ., 2013). However, careful studies by the Tan and Sutterlin group convincingly demonstrated that the majority of CPAF activity in infected cells is actually sequestered in the chlamydial inclusion and that biochemical assays relying on cell homogenization in many cases released the sequestered CPAF allowing degradation of ‘targets’ that would not interact with CPAF under biological conditions (Chen et al ., 2012). Thus, the question becomes not what host proteins does CPAF cleave but what host proteins does CPAF have access to and when does it gain this access. New data from the investigation of growth and virulence phenotypes of two mutant strains of chlamydia null for CPAF activity isolated by Emily Snavely in the Valdivia laboratory have added critical observations that have evolved our understanding of the role of CPAF in pathogenesis (Snavely et al ., 2014). The Valdivia laboratory observed that CPAF null strains follow the same developmental cycle and produce normal appearing …